Multiple sequence alignment - TraesCS5D01G256300

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS5D01G256300 chr5D 100.000 7608 0 0 1 7608 362574354 362581961 0.000000e+00 14050.0
1 TraesCS5D01G256300 chr5A 96.131 3903 102 25 3440 7319 463600611 463604487 0.000000e+00 6325.0
2 TraesCS5D01G256300 chr5A 94.978 3465 114 28 3 3441 463597099 463600529 0.000000e+00 5380.0
3 TraesCS5D01G256300 chr5A 92.157 204 14 2 4935 5137 357050964 357050762 3.470000e-73 287.0
4 TraesCS5D01G256300 chr5B 93.679 3180 122 25 3 3157 428574223 428577348 0.000000e+00 4686.0
5 TraesCS5D01G256300 chr5B 93.147 1182 50 15 6163 7319 428580902 428582077 0.000000e+00 1705.0
6 TraesCS5D01G256300 chr5B 90.658 942 69 12 5144 6077 428579933 428580863 0.000000e+00 1234.0
7 TraesCS5D01G256300 chr5B 90.880 625 53 2 3698 4318 428578126 428578750 0.000000e+00 835.0
8 TraesCS5D01G256300 chr5B 92.800 250 14 4 4379 4624 428578767 428579016 7.260000e-95 359.0
9 TraesCS5D01G256300 chr5B 88.462 286 24 4 3156 3440 428577430 428577707 3.400000e-88 337.0
10 TraesCS5D01G256300 chr5B 91.257 183 13 3 4647 4827 428579363 428579544 5.900000e-61 246.0
11 TraesCS5D01G256300 chr5B 93.913 115 6 1 3619 3732 428577929 428578043 1.010000e-38 172.0
12 TraesCS5D01G256300 chr5B 92.308 117 8 1 4821 4937 428579806 428579921 1.700000e-36 165.0
13 TraesCS5D01G256300 chr4D 95.050 202 9 1 4935 5136 258893653 258893453 4.430000e-82 316.0
14 TraesCS5D01G256300 chr4D 88.971 136 13 2 7472 7606 70500806 70500672 4.720000e-37 167.0
15 TraesCS5D01G256300 chr4D 93.846 65 4 0 7318 7382 343547658 343547722 1.750000e-16 99.0
16 TraesCS5D01G256300 chr3D 91.593 226 15 4 4924 5147 317203383 317203606 7.410000e-80 309.0
17 TraesCS5D01G256300 chr6D 92.718 206 12 3 4935 5140 181729735 181729533 2.080000e-75 294.0
18 TraesCS5D01G256300 chr2D 92.683 205 14 1 4935 5139 647674607 647674810 2.080000e-75 294.0
19 TraesCS5D01G256300 chr2D 88.489 139 15 1 7470 7607 31604695 31604833 4.720000e-37 167.0
20 TraesCS5D01G256300 chr7A 93.434 198 9 4 4937 5134 504221546 504221353 2.690000e-74 291.0
21 TraesCS5D01G256300 chr7A 89.928 139 11 3 7467 7603 680570670 680570533 7.850000e-40 176.0
22 TraesCS5D01G256300 chr7A 88.652 141 11 4 7471 7607 528292212 528292073 4.720000e-37 167.0
23 TraesCS5D01G256300 chr3B 92.611 203 12 3 4935 5136 471249082 471248882 9.660000e-74 289.0
24 TraesCS5D01G256300 chr3B 88.194 144 11 5 7470 7608 761334928 761335070 4.720000e-37 167.0
25 TraesCS5D01G256300 chr1B 93.434 198 7 2 4937 5134 48276320 48276129 9.660000e-74 289.0
26 TraesCS5D01G256300 chr7D 88.811 143 12 3 7470 7608 209575279 209575137 1.010000e-38 172.0
27 TraesCS5D01G256300 chr7D 88.112 143 12 3 7470 7608 393623781 393623640 1.700000e-36 165.0
28 TraesCS5D01G256300 chr7B 89.286 140 11 3 7473 7608 522085162 522085023 1.010000e-38 172.0
29 TraesCS5D01G256300 chr3A 90.840 131 9 3 7470 7598 746225279 746225150 1.010000e-38 172.0
30 TraesCS5D01G256300 chr2B 90.909 66 6 0 7317 7382 457328969 457328904 1.050000e-13 89.8
31 TraesCS5D01G256300 chr2A 97.826 46 1 0 7337 7382 239369808 239369853 6.330000e-11 80.5
32 TraesCS5D01G256300 chr6B 100.000 38 0 0 7316 7353 668924431 668924468 3.810000e-08 71.3
33 TraesCS5D01G256300 chr6B 86.154 65 9 0 7318 7382 682126567 682126503 3.810000e-08 71.3
34 TraesCS5D01G256300 chr4A 87.037 54 7 0 7316 7369 619137101 619137048 2.290000e-05 62.1


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G256300 chr5D 362574354 362581961 7607 False 14050.000000 14050 100.000000 1 7608 1 chr5D.!!$F1 7607
1 TraesCS5D01G256300 chr5A 463597099 463604487 7388 False 5852.500000 6325 95.554500 3 7319 2 chr5A.!!$F1 7316
2 TraesCS5D01G256300 chr5B 428574223 428582077 7854 False 1082.111111 4686 91.900444 3 7319 9 chr5B.!!$F1 7316

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
650 673 0.172803 CCGCCCACACTGACTAGTAC 59.827 60.000 0.00 0.00 34.74 2.73 F
1656 1708 0.106819 ACATGGCTGCCCTCTTCATC 60.107 55.000 17.53 0.00 0.00 2.92 F
1989 2041 1.164041 GGTGTTTGAGTCGGTGGTGG 61.164 60.000 0.00 0.00 0.00 4.61 F
1990 2042 1.525077 TGTTTGAGTCGGTGGTGGC 60.525 57.895 0.00 0.00 0.00 5.01 F
2026 2078 1.739067 AAGAATGCGCACTTACCCTC 58.261 50.000 14.90 0.63 0.00 4.30 F
3367 3503 1.526464 CCTTTGCACATTTTCAACGCC 59.474 47.619 0.00 0.00 0.00 5.68 F
3841 4259 0.325602 TCACATGGACAGATGCAGCA 59.674 50.000 4.07 0.00 0.00 4.41 F
4141 4559 0.453793 CTCTTCATCACGCTCGAGGT 59.546 55.000 15.58 7.66 0.00 3.85 F
5042 6057 0.663153 GGCAGGTGCTTAATTAGGCG 59.337 55.000 14.11 2.06 41.70 5.52 F
6217 7251 0.388649 ACTAGAGAACAGTTGCCGCG 60.389 55.000 0.00 0.00 0.00 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2008 2060 0.613260 TGAGGGTAAGTGCGCATTCT 59.387 50.000 15.91 3.36 0.00 2.40 R
2914 2966 4.089361 AGGGGAACAAAGCAATTTCTAGG 58.911 43.478 0.00 0.00 0.00 3.02 R
3367 3503 4.724074 ACCACAAAATGCATGTATCCAG 57.276 40.909 0.00 0.00 0.00 3.86 R
3368 3504 5.451659 GCATACCACAAAATGCATGTATCCA 60.452 40.000 0.00 0.00 46.19 3.41 R
3839 4257 6.624352 ACAATGTGGATTGACACTATATGC 57.376 37.500 0.00 0.00 41.49 3.14 R
5005 6020 1.400494 GCCCTGTACAAATAAGCACCG 59.600 52.381 0.00 0.00 0.00 4.94 R
5616 6635 1.732259 CCCAAAGAAATCAGACCGTCG 59.268 52.381 0.00 0.00 0.00 5.12 R
6089 7111 0.383590 TGAGATGCGCAGAGAGTAGC 59.616 55.000 18.32 0.00 0.00 3.58 R
6486 7522 1.902508 CAGGAAGACTGGGTAAGCAGA 59.097 52.381 0.00 0.00 43.70 4.26 R
7454 8507 0.036765 AATGCGGACGTAGGAAGCAA 60.037 50.000 6.90 0.00 41.37 3.91 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 1.134401 TGCTGCTGGTACTGGATTAGC 60.134 52.381 0.00 0.00 35.06 3.09
78 79 5.692204 AGCAAAGTGTATATTCTCCGATTCG 59.308 40.000 0.00 0.00 0.00 3.34
94 95 3.857093 CGATTCGCCCCTTTTGTTAATTG 59.143 43.478 0.00 0.00 0.00 2.32
144 148 7.224167 GTGGTGGTTAGAAACTTAGAATATCCG 59.776 40.741 0.00 0.00 0.00 4.18
145 149 6.704937 GGTGGTTAGAAACTTAGAATATCCGG 59.295 42.308 0.00 0.00 0.00 5.14
186 190 7.813148 GTGTTAATAAAGAGAAAAAGCCTTCCC 59.187 37.037 0.00 0.00 0.00 3.97
189 193 2.481289 AGAGAAAAAGCCTTCCCTCG 57.519 50.000 0.00 0.00 0.00 4.63
220 224 5.401376 TCTGACGAGACATAGAAAACAAACG 59.599 40.000 0.00 0.00 0.00 3.60
263 273 2.023741 CCAGCGATGCGATGCAAC 59.976 61.111 0.00 0.00 43.62 4.17
264 274 2.466982 CCAGCGATGCGATGCAACT 61.467 57.895 0.00 0.00 43.62 3.16
265 275 1.011463 CAGCGATGCGATGCAACTC 60.011 57.895 0.00 0.00 43.62 3.01
266 276 1.153489 AGCGATGCGATGCAACTCT 60.153 52.632 0.00 0.00 43.62 3.24
397 408 2.031157 CGGTGGGTTCACAACTGAATTC 60.031 50.000 0.00 0.00 45.32 2.17
513 535 0.531200 ACGAGTCGGAGGTCAATTCC 59.469 55.000 18.30 0.00 0.00 3.01
646 669 1.835267 ACACCGCCCACACTGACTA 60.835 57.895 0.00 0.00 0.00 2.59
650 673 0.172803 CCGCCCACACTGACTAGTAC 59.827 60.000 0.00 0.00 34.74 2.73
651 674 1.174783 CGCCCACACTGACTAGTACT 58.825 55.000 0.00 0.00 34.74 2.73
652 675 2.362736 CGCCCACACTGACTAGTACTA 58.637 52.381 1.89 1.89 34.74 1.82
653 676 2.355132 CGCCCACACTGACTAGTACTAG 59.645 54.545 25.30 25.30 34.74 2.57
770 798 2.424341 CGTTTCCGCGCAGTAAATAAC 58.576 47.619 8.75 0.46 0.00 1.89
771 799 2.159814 CGTTTCCGCGCAGTAAATAACA 60.160 45.455 8.75 0.00 0.00 2.41
772 800 3.413558 GTTTCCGCGCAGTAAATAACAG 58.586 45.455 8.75 0.00 0.00 3.16
773 801 1.003851 TCCGCGCAGTAAATAACAGC 58.996 50.000 8.75 0.00 37.26 4.40
774 802 1.006832 CCGCGCAGTAAATAACAGCT 58.993 50.000 8.75 0.00 38.40 4.24
775 803 1.004927 CCGCGCAGTAAATAACAGCTC 60.005 52.381 8.75 0.00 38.40 4.09
776 804 1.658596 CGCGCAGTAAATAACAGCTCA 59.341 47.619 8.75 0.00 38.40 4.26
784 814 0.676782 AATAACAGCTCACCCCGTGC 60.677 55.000 0.00 0.00 32.98 5.34
785 815 1.553690 ATAACAGCTCACCCCGTGCT 61.554 55.000 0.00 0.00 45.21 4.40
809 839 2.104281 ACTCGTCCACTGCTTTTTACCT 59.896 45.455 0.00 0.00 0.00 3.08
847 877 5.393866 TGCCCCTTTTATCACTCTCTTTTT 58.606 37.500 0.00 0.00 0.00 1.94
848 878 5.476945 TGCCCCTTTTATCACTCTCTTTTTC 59.523 40.000 0.00 0.00 0.00 2.29
849 879 5.712446 GCCCCTTTTATCACTCTCTTTTTCT 59.288 40.000 0.00 0.00 0.00 2.52
926 959 3.646715 CCAAGGGACAGCGGGGAA 61.647 66.667 0.00 0.00 0.00 3.97
1464 1510 3.945434 GTCGCCATGCTCATGCGG 61.945 66.667 18.78 8.53 43.34 5.69
1580 1631 1.381735 CTTTGGATTGGGGGAGCCC 60.382 63.158 0.00 0.00 44.51 5.19
1586 1637 2.893682 GATTGGGGGAGCCCGAGTTG 62.894 65.000 0.00 0.00 46.66 3.16
1628 1680 7.785506 TCTTCTTTTTGGGGGTTATTACTTTGA 59.214 33.333 0.00 0.00 0.00 2.69
1656 1708 0.106819 ACATGGCTGCCCTCTTCATC 60.107 55.000 17.53 0.00 0.00 2.92
1989 2041 1.164041 GGTGTTTGAGTCGGTGGTGG 61.164 60.000 0.00 0.00 0.00 4.61
1990 2042 1.525077 TGTTTGAGTCGGTGGTGGC 60.525 57.895 0.00 0.00 0.00 5.01
2008 2060 2.158682 TGGCCTGAGCTTGTCAAGTAAA 60.159 45.455 14.03 0.00 39.73 2.01
2009 2061 2.485814 GGCCTGAGCTTGTCAAGTAAAG 59.514 50.000 14.03 8.54 39.73 1.85
2014 2066 5.362556 TGAGCTTGTCAAGTAAAGAATGC 57.637 39.130 14.03 0.00 29.64 3.56
2017 2069 3.609175 GCTTGTCAAGTAAAGAATGCGCA 60.609 43.478 14.96 14.96 0.00 6.09
2026 2078 1.739067 AAGAATGCGCACTTACCCTC 58.261 50.000 14.90 0.63 0.00 4.30
2094 2146 6.211184 TGAATTGTGCCACCTTCTCAATTTAT 59.789 34.615 8.23 0.00 37.59 1.40
2120 2172 5.163195 ACAGCAATGAACCTATTAGGGGTAG 60.163 44.000 14.26 0.72 40.58 3.18
2121 2173 4.975794 AGCAATGAACCTATTAGGGGTAGT 59.024 41.667 14.26 0.00 40.58 2.73
2122 2174 6.042781 CAGCAATGAACCTATTAGGGGTAGTA 59.957 42.308 14.26 0.00 40.58 1.82
2138 2190 6.161170 AGGGGTAGTACATAGTAGTACCAAGT 59.839 42.308 28.76 16.92 44.19 3.16
2229 2281 3.407698 TGGATTGTGCAACTTATCGTGT 58.592 40.909 0.00 0.00 38.04 4.49
2237 2289 5.994887 TGCAACTTATCGTGTTGTACTTT 57.005 34.783 8.15 0.00 44.54 2.66
2608 2660 9.765795 AATTTTCTATTCCTCTAGTTATCACCG 57.234 33.333 0.00 0.00 0.00 4.94
2918 2970 3.139565 GCGGTAAGCCCCTCCTAG 58.860 66.667 0.00 0.00 40.81 3.02
3048 3100 6.238402 CCATTTGACAGACTTGATGCTGATAG 60.238 42.308 0.00 0.00 36.07 2.08
3367 3503 1.526464 CCTTTGCACATTTTCAACGCC 59.474 47.619 0.00 0.00 0.00 5.68
3368 3504 2.472816 CTTTGCACATTTTCAACGCCT 58.527 42.857 0.00 0.00 0.00 5.52
3419 3555 7.817478 TCACTAATCACTATGTTGTGTTACTGG 59.183 37.037 0.00 0.00 38.90 4.00
3513 3809 7.147567 TGCATATGAGTGTATACCTTTTCTCCA 60.148 37.037 6.97 0.00 0.00 3.86
3582 3878 7.367285 TGAGTACATGTATTTGAAAAAGGCAC 58.633 34.615 9.18 0.00 0.00 5.01
3732 4146 2.070783 CTGCGAAATTGGCAAATTGCT 58.929 42.857 18.04 0.00 44.28 3.91
3733 4147 3.252400 CTGCGAAATTGGCAAATTGCTA 58.748 40.909 18.04 9.20 44.28 3.49
3756 4174 9.250624 GCTAATATGTTCAGACCTTACTACAAG 57.749 37.037 0.00 0.00 0.00 3.16
3841 4259 0.325602 TCACATGGACAGATGCAGCA 59.674 50.000 4.07 0.00 0.00 4.41
3882 4300 9.566432 ACATTGTTCTCTTTTCTCTATTTCTGT 57.434 29.630 0.00 0.00 0.00 3.41
4065 4483 8.718102 TTGATTAGATTTCCCTTCTAACTTCG 57.282 34.615 0.00 0.00 38.23 3.79
4141 4559 0.453793 CTCTTCATCACGCTCGAGGT 59.546 55.000 15.58 7.66 0.00 3.85
4187 4605 3.161866 AGCCAAATTCACATACCGGTTT 58.838 40.909 15.04 0.14 0.00 3.27
4566 4984 4.355543 AATTGTTACCATGATGCGTGAC 57.644 40.909 0.00 0.00 0.00 3.67
4571 4989 2.779755 ACCATGATGCGTGACCTTTA 57.220 45.000 0.00 0.00 0.00 1.85
4592 5011 8.451748 CCTTTAATTGTTTCTTAGCTACCAGAC 58.548 37.037 0.00 0.00 0.00 3.51
4875 5890 3.129638 GGCTCTAGGTGTAGTGAACTCAG 59.870 52.174 0.00 0.00 0.00 3.35
4930 5945 3.052036 CAGAAAACATCCAAACTTGCCG 58.948 45.455 0.00 0.00 0.00 5.69
4954 5969 3.891977 TGTTAGGCCTTTGTACAATGCAA 59.108 39.130 23.88 12.99 0.00 4.08
4955 5970 4.022416 TGTTAGGCCTTTGTACAATGCAAG 60.022 41.667 23.88 13.32 0.00 4.01
4956 5971 1.895131 AGGCCTTTGTACAATGCAAGG 59.105 47.619 23.88 20.51 0.00 3.61
4957 5972 1.618343 GGCCTTTGTACAATGCAAGGT 59.382 47.619 23.88 0.00 0.00 3.50
4958 5973 2.610232 GGCCTTTGTACAATGCAAGGTG 60.610 50.000 23.88 9.62 0.00 4.00
4959 5974 2.676076 CCTTTGTACAATGCAAGGTGC 58.324 47.619 9.56 0.00 45.29 5.01
4960 5975 2.297033 CCTTTGTACAATGCAAGGTGCT 59.703 45.455 9.56 0.00 45.31 4.40
4961 5976 3.243839 CCTTTGTACAATGCAAGGTGCTT 60.244 43.478 9.56 0.00 45.31 3.91
4962 5977 4.022416 CCTTTGTACAATGCAAGGTGCTTA 60.022 41.667 9.56 0.00 45.31 3.09
4963 5978 5.508825 CCTTTGTACAATGCAAGGTGCTTAA 60.509 40.000 9.56 4.79 45.31 1.85
4964 5979 4.764679 TGTACAATGCAAGGTGCTTAAG 57.235 40.909 9.81 0.00 45.31 1.85
4965 5980 4.393834 TGTACAATGCAAGGTGCTTAAGA 58.606 39.130 6.67 0.00 45.31 2.10
4966 5981 4.455533 TGTACAATGCAAGGTGCTTAAGAG 59.544 41.667 6.67 0.00 45.31 2.85
5028 6043 2.423538 GTGCTTATTTGTACAGGGCAGG 59.576 50.000 0.00 0.00 0.00 4.85
5029 6044 2.041081 TGCTTATTTGTACAGGGCAGGT 59.959 45.455 0.00 0.00 0.00 4.00
5042 6057 0.663153 GGCAGGTGCTTAATTAGGCG 59.337 55.000 14.11 2.06 41.70 5.52
5049 6064 3.124560 GTGCTTAATTAGGCGTCTCTCC 58.875 50.000 14.11 0.00 0.00 3.71
5107 6122 7.110155 TCGGTTTATTTTTCTAAGCATCTCCT 58.890 34.615 0.00 0.00 0.00 3.69
5200 6215 4.082787 GCTAGTTGCTTTCCTTGCACATAA 60.083 41.667 0.00 0.00 40.40 1.90
5230 6245 7.429374 TTGCATTTGATTGGTATAATTCCCA 57.571 32.000 0.00 0.00 0.00 4.37
5641 6660 2.232208 GGTCTGATTTCTTTGGGCTTGG 59.768 50.000 0.00 0.00 0.00 3.61
5731 6750 4.338012 TCAGCACATCTGTTGGATTGAAT 58.662 39.130 0.00 0.00 43.32 2.57
6072 7094 8.726988 TCCATTTGTAGTCCTTTCTTTAAATCG 58.273 33.333 0.00 0.00 0.00 3.34
6132 7154 4.761975 CATGCAAGTTATTTGGGCTTCAT 58.238 39.130 0.00 0.00 37.26 2.57
6140 7162 6.945218 AGTTATTTGGGCTTCATAAATGCAA 58.055 32.000 0.00 0.00 0.00 4.08
6217 7251 0.388649 ACTAGAGAACAGTTGCCGCG 60.389 55.000 0.00 0.00 0.00 6.46
6281 7317 7.387673 GGTTGGCTTGCTAGATAAATTTTTGTT 59.612 33.333 0.00 0.00 0.00 2.83
6445 7481 3.885484 ATTTTCTGTCGAGCAGTGTTG 57.115 42.857 12.62 0.00 45.23 3.33
6486 7522 1.949525 GCATGGCGAACATCTACCAAT 59.050 47.619 0.00 0.00 37.84 3.16
6616 7652 3.488721 GCAACAGGACATGATGATCAAGC 60.489 47.826 0.00 0.00 33.68 4.01
7008 8046 3.395639 AGCTCCATGTTTTGCATTGTTG 58.604 40.909 0.00 0.00 35.19 3.33
7078 8116 2.344872 GGGTTCCGCGTACCTGTT 59.655 61.111 22.14 0.00 35.92 3.16
7334 8387 2.822399 GGGACCTCCTATGTGCCG 59.178 66.667 0.00 0.00 34.40 5.69
7335 8388 2.109181 GGACCTCCTATGTGCCGC 59.891 66.667 0.00 0.00 0.00 6.53
7336 8389 2.435693 GGACCTCCTATGTGCCGCT 61.436 63.158 0.00 0.00 0.00 5.52
7337 8390 1.522569 GACCTCCTATGTGCCGCTT 59.477 57.895 0.00 0.00 0.00 4.68
7338 8391 0.750850 GACCTCCTATGTGCCGCTTA 59.249 55.000 0.00 0.00 0.00 3.09
7339 8392 1.344763 GACCTCCTATGTGCCGCTTAT 59.655 52.381 0.00 0.00 0.00 1.73
7340 8393 1.768870 ACCTCCTATGTGCCGCTTATT 59.231 47.619 0.00 0.00 0.00 1.40
7341 8394 2.146342 CCTCCTATGTGCCGCTTATTG 58.854 52.381 0.00 0.00 0.00 1.90
7342 8395 1.532868 CTCCTATGTGCCGCTTATTGC 59.467 52.381 0.00 0.00 38.57 3.56
7352 8405 2.482326 GCTTATTGCGGCAAGGAGT 58.518 52.632 21.11 6.67 0.00 3.85
7353 8406 0.811281 GCTTATTGCGGCAAGGAGTT 59.189 50.000 21.11 6.28 0.00 3.01
7354 8407 1.468054 GCTTATTGCGGCAAGGAGTTG 60.468 52.381 21.11 8.63 36.67 3.16
7375 8428 3.999229 CAGTTTTGCATAGGAGACGAC 57.001 47.619 0.00 0.00 0.00 4.34
7376 8429 3.589988 CAGTTTTGCATAGGAGACGACT 58.410 45.455 0.00 0.00 0.00 4.18
7377 8430 3.614616 CAGTTTTGCATAGGAGACGACTC 59.385 47.826 6.33 6.33 41.94 3.36
7378 8431 3.258372 AGTTTTGCATAGGAGACGACTCA 59.742 43.478 16.47 0.00 44.22 3.41
7379 8432 2.941453 TTGCATAGGAGACGACTCAC 57.059 50.000 16.47 6.30 44.22 3.51
7380 8433 1.103803 TGCATAGGAGACGACTCACC 58.896 55.000 16.47 0.91 44.22 4.02
7381 8434 1.341089 TGCATAGGAGACGACTCACCT 60.341 52.381 16.47 8.59 44.22 4.00
7382 8435 1.335496 GCATAGGAGACGACTCACCTC 59.665 57.143 16.47 0.00 44.22 3.85
7383 8436 1.950909 CATAGGAGACGACTCACCTCC 59.049 57.143 16.47 8.47 45.16 4.30
7384 8437 3.188965 GGAGACGACTCACCTCCG 58.811 66.667 16.47 0.00 44.22 4.63
7385 8438 2.486042 GAGACGACTCACCTCCGC 59.514 66.667 10.08 0.00 42.21 5.54
7386 8439 2.282251 AGACGACTCACCTCCGCA 60.282 61.111 0.00 0.00 0.00 5.69
7387 8440 2.179517 GACGACTCACCTCCGCAG 59.820 66.667 0.00 0.00 0.00 5.18
7388 8441 2.282251 ACGACTCACCTCCGCAGA 60.282 61.111 0.00 0.00 0.00 4.26
7389 8442 1.863662 GACGACTCACCTCCGCAGAA 61.864 60.000 0.00 0.00 0.00 3.02
7390 8443 1.251527 ACGACTCACCTCCGCAGAAT 61.252 55.000 0.00 0.00 0.00 2.40
7391 8444 0.803768 CGACTCACCTCCGCAGAATG 60.804 60.000 0.00 0.00 40.87 2.67
7392 8445 0.532573 GACTCACCTCCGCAGAATGA 59.467 55.000 0.00 0.00 39.69 2.57
7393 8446 0.976641 ACTCACCTCCGCAGAATGAA 59.023 50.000 0.00 0.00 39.69 2.57
7394 8447 1.347707 ACTCACCTCCGCAGAATGAAA 59.652 47.619 0.00 0.00 39.69 2.69
7395 8448 2.224523 ACTCACCTCCGCAGAATGAAAA 60.225 45.455 0.00 0.00 39.69 2.29
7396 8449 2.813754 CTCACCTCCGCAGAATGAAAAA 59.186 45.455 0.00 0.00 39.69 1.94
7397 8450 3.420893 TCACCTCCGCAGAATGAAAAAT 58.579 40.909 0.00 0.00 39.69 1.82
7398 8451 3.440173 TCACCTCCGCAGAATGAAAAATC 59.560 43.478 0.00 0.00 39.69 2.17
7399 8452 2.420022 ACCTCCGCAGAATGAAAAATCG 59.580 45.455 0.00 0.00 39.69 3.34
7400 8453 2.444351 CTCCGCAGAATGAAAAATCGC 58.556 47.619 0.00 0.00 39.69 4.58
7401 8454 1.809547 TCCGCAGAATGAAAAATCGCA 59.190 42.857 0.00 0.00 39.69 5.10
7402 8455 2.227626 TCCGCAGAATGAAAAATCGCAA 59.772 40.909 0.00 0.00 39.69 4.85
7403 8456 2.985809 CCGCAGAATGAAAAATCGCAAA 59.014 40.909 0.00 0.00 39.69 3.68
7404 8457 3.428198 CCGCAGAATGAAAAATCGCAAAA 59.572 39.130 0.00 0.00 39.69 2.44
7405 8458 4.084641 CCGCAGAATGAAAAATCGCAAAAA 60.085 37.500 0.00 0.00 39.69 1.94
7406 8459 5.389725 CCGCAGAATGAAAAATCGCAAAAAT 60.390 36.000 0.00 0.00 39.69 1.82
7407 8460 6.183360 CCGCAGAATGAAAAATCGCAAAAATA 60.183 34.615 0.00 0.00 39.69 1.40
7408 8461 7.226084 CGCAGAATGAAAAATCGCAAAAATAA 58.774 30.769 0.00 0.00 39.69 1.40
7409 8462 7.739477 CGCAGAATGAAAAATCGCAAAAATAAA 59.261 29.630 0.00 0.00 39.69 1.40
7410 8463 9.379811 GCAGAATGAAAAATCGCAAAAATAAAA 57.620 25.926 0.00 0.00 39.69 1.52
7418 8471 8.760703 AAAATCGCAAAAATAAAAGGAAAACG 57.239 26.923 0.00 0.00 0.00 3.60
7419 8472 7.471657 AATCGCAAAAATAAAAGGAAAACGT 57.528 28.000 0.00 0.00 0.00 3.99
7420 8473 6.889019 TCGCAAAAATAAAAGGAAAACGTT 57.111 29.167 0.00 0.00 0.00 3.99
7421 8474 6.697152 TCGCAAAAATAAAAGGAAAACGTTG 58.303 32.000 0.00 0.00 0.00 4.10
7422 8475 5.899151 CGCAAAAATAAAAGGAAAACGTTGG 59.101 36.000 0.00 0.00 0.00 3.77
7423 8476 6.455780 CGCAAAAATAAAAGGAAAACGTTGGT 60.456 34.615 0.00 0.00 0.00 3.67
7424 8477 6.684979 GCAAAAATAAAAGGAAAACGTTGGTG 59.315 34.615 0.00 0.00 0.00 4.17
7425 8478 6.912203 AAAATAAAAGGAAAACGTTGGTGG 57.088 33.333 0.00 0.00 0.00 4.61
7426 8479 2.303163 AAAAGGAAAACGTTGGTGGC 57.697 45.000 0.00 0.00 0.00 5.01
7427 8480 0.462375 AAAGGAAAACGTTGGTGGCC 59.538 50.000 0.00 0.00 0.00 5.36
7428 8481 1.730451 AAGGAAAACGTTGGTGGCCG 61.730 55.000 0.00 0.00 0.00 6.13
7429 8482 2.333581 GAAAACGTTGGTGGCCGG 59.666 61.111 0.00 0.00 0.00 6.13
7430 8483 2.440613 AAAACGTTGGTGGCCGGT 60.441 55.556 0.00 0.00 0.00 5.28
7431 8484 2.671357 GAAAACGTTGGTGGCCGGTG 62.671 60.000 0.00 0.00 0.00 4.94
7462 8515 4.394712 CTCGGCCGGTTGCTTCCT 62.395 66.667 27.83 0.00 40.92 3.36
7463 8516 2.998480 TCGGCCGGTTGCTTCCTA 60.998 61.111 27.83 0.00 40.92 2.94
7464 8517 2.818274 CGGCCGGTTGCTTCCTAC 60.818 66.667 20.10 0.00 40.92 3.18
7465 8518 2.818274 GGCCGGTTGCTTCCTACG 60.818 66.667 1.90 0.00 40.92 3.51
7466 8519 2.047560 GCCGGTTGCTTCCTACGT 60.048 61.111 1.90 0.00 36.87 3.57
7467 8520 2.098831 GCCGGTTGCTTCCTACGTC 61.099 63.158 1.90 0.00 36.87 4.34
7468 8521 1.447314 CCGGTTGCTTCCTACGTCC 60.447 63.158 0.00 0.00 0.00 4.79
7469 8522 1.804326 CGGTTGCTTCCTACGTCCG 60.804 63.158 0.00 0.00 0.00 4.79
7470 8523 2.098831 GGTTGCTTCCTACGTCCGC 61.099 63.158 0.00 0.00 0.00 5.54
7471 8524 1.373748 GTTGCTTCCTACGTCCGCA 60.374 57.895 0.00 0.00 0.00 5.69
7472 8525 0.739813 GTTGCTTCCTACGTCCGCAT 60.740 55.000 0.00 0.00 0.00 4.73
7473 8526 0.036765 TTGCTTCCTACGTCCGCATT 60.037 50.000 0.00 0.00 0.00 3.56
7474 8527 0.036765 TGCTTCCTACGTCCGCATTT 60.037 50.000 0.00 0.00 0.00 2.32
7475 8528 0.651031 GCTTCCTACGTCCGCATTTC 59.349 55.000 0.00 0.00 0.00 2.17
7476 8529 1.287425 CTTCCTACGTCCGCATTTCC 58.713 55.000 0.00 0.00 0.00 3.13
7477 8530 0.899720 TTCCTACGTCCGCATTTCCT 59.100 50.000 0.00 0.00 0.00 3.36
7478 8531 1.766494 TCCTACGTCCGCATTTCCTA 58.234 50.000 0.00 0.00 0.00 2.94
7479 8532 2.313317 TCCTACGTCCGCATTTCCTAT 58.687 47.619 0.00 0.00 0.00 2.57
7480 8533 2.696707 TCCTACGTCCGCATTTCCTATT 59.303 45.455 0.00 0.00 0.00 1.73
7481 8534 3.133362 TCCTACGTCCGCATTTCCTATTT 59.867 43.478 0.00 0.00 0.00 1.40
7482 8535 3.247648 CCTACGTCCGCATTTCCTATTTG 59.752 47.826 0.00 0.00 0.00 2.32
7483 8536 2.980568 ACGTCCGCATTTCCTATTTGA 58.019 42.857 0.00 0.00 0.00 2.69
7484 8537 2.676342 ACGTCCGCATTTCCTATTTGAC 59.324 45.455 0.00 0.00 0.00 3.18
7485 8538 2.285602 CGTCCGCATTTCCTATTTGACG 60.286 50.000 0.00 0.00 38.42 4.35
7486 8539 1.668751 TCCGCATTTCCTATTTGACGC 59.331 47.619 0.00 0.00 0.00 5.19
7487 8540 1.268539 CCGCATTTCCTATTTGACGCC 60.269 52.381 0.00 0.00 0.00 5.68
7488 8541 1.400142 CGCATTTCCTATTTGACGCCA 59.600 47.619 0.00 0.00 0.00 5.69
7489 8542 2.791158 CGCATTTCCTATTTGACGCCAC 60.791 50.000 0.00 0.00 0.00 5.01
7490 8543 2.163412 GCATTTCCTATTTGACGCCACA 59.837 45.455 0.00 0.00 0.00 4.17
7491 8544 3.731867 GCATTTCCTATTTGACGCCACAG 60.732 47.826 0.00 0.00 0.00 3.66
7492 8545 2.107950 TTCCTATTTGACGCCACAGG 57.892 50.000 0.00 0.00 0.00 4.00
7493 8546 0.392461 TCCTATTTGACGCCACAGGC 60.392 55.000 0.00 0.00 46.75 4.85
7502 8555 2.671619 GCCACAGGCGCCAGTTAA 60.672 61.111 31.54 0.00 39.62 2.01
7503 8556 2.978018 GCCACAGGCGCCAGTTAAC 61.978 63.158 31.54 14.34 39.62 2.01
7504 8557 2.677003 CCACAGGCGCCAGTTAACG 61.677 63.158 31.54 14.62 0.00 3.18
7505 8558 1.959226 CACAGGCGCCAGTTAACGT 60.959 57.895 31.54 10.51 0.00 3.99
7506 8559 1.959226 ACAGGCGCCAGTTAACGTG 60.959 57.895 31.54 17.94 0.00 4.49
7507 8560 3.047877 AGGCGCCAGTTAACGTGC 61.048 61.111 31.54 9.69 34.73 5.34
7508 8561 3.350612 GGCGCCAGTTAACGTGCA 61.351 61.111 24.80 0.00 37.23 4.57
7509 8562 2.686816 GGCGCCAGTTAACGTGCAT 61.687 57.895 24.80 0.00 37.23 3.96
7510 8563 1.209127 GCGCCAGTTAACGTGCATT 59.791 52.632 18.33 0.00 35.57 3.56
7511 8564 0.386731 GCGCCAGTTAACGTGCATTT 60.387 50.000 18.33 0.00 35.57 2.32
7512 8565 1.928595 GCGCCAGTTAACGTGCATTTT 60.929 47.619 18.33 0.00 35.57 1.82
7513 8566 1.976045 CGCCAGTTAACGTGCATTTTC 59.024 47.619 18.33 0.00 0.00 2.29
7514 8567 2.603412 CGCCAGTTAACGTGCATTTTCA 60.603 45.455 18.33 0.00 0.00 2.69
7515 8568 3.574614 GCCAGTTAACGTGCATTTTCAT 58.425 40.909 14.91 0.00 0.00 2.57
7516 8569 3.987220 GCCAGTTAACGTGCATTTTCATT 59.013 39.130 14.91 0.00 0.00 2.57
7517 8570 5.157781 GCCAGTTAACGTGCATTTTCATTA 58.842 37.500 14.91 0.00 0.00 1.90
7518 8571 5.631512 GCCAGTTAACGTGCATTTTCATTAA 59.368 36.000 14.91 0.00 0.00 1.40
7519 8572 6.399564 GCCAGTTAACGTGCATTTTCATTAAC 60.400 38.462 14.91 0.00 34.31 2.01
7520 8573 6.861055 CCAGTTAACGTGCATTTTCATTAACT 59.139 34.615 0.00 0.00 41.30 2.24
7521 8574 7.710273 CAGTTAACGTGCATTTTCATTAACTG 58.290 34.615 15.01 15.01 46.11 3.16
7522 8575 6.861055 AGTTAACGTGCATTTTCATTAACTGG 59.139 34.615 5.72 0.00 39.91 4.00
7523 8576 4.846779 ACGTGCATTTTCATTAACTGGT 57.153 36.364 0.00 0.00 0.00 4.00
7524 8577 4.545610 ACGTGCATTTTCATTAACTGGTG 58.454 39.130 0.00 0.00 0.00 4.17
7525 8578 3.364621 CGTGCATTTTCATTAACTGGTGC 59.635 43.478 0.00 0.00 0.00 5.01
7526 8579 3.679502 GTGCATTTTCATTAACTGGTGCC 59.320 43.478 0.00 0.00 0.00 5.01
7527 8580 3.577848 TGCATTTTCATTAACTGGTGCCT 59.422 39.130 0.00 0.00 0.00 4.75
7528 8581 3.928375 GCATTTTCATTAACTGGTGCCTG 59.072 43.478 0.00 0.00 0.00 4.85
7529 8582 4.561326 GCATTTTCATTAACTGGTGCCTGT 60.561 41.667 0.00 0.00 0.00 4.00
7530 8583 4.582701 TTTTCATTAACTGGTGCCTGTG 57.417 40.909 1.52 0.00 0.00 3.66
7531 8584 2.198827 TCATTAACTGGTGCCTGTGG 57.801 50.000 1.52 0.00 0.00 4.17
7541 8594 2.125269 GCCTGTGGCGTCCGTAAT 60.125 61.111 0.00 0.00 39.62 1.89
7542 8595 2.461110 GCCTGTGGCGTCCGTAATG 61.461 63.158 0.00 0.00 39.62 1.90
7543 8596 1.813753 CCTGTGGCGTCCGTAATGG 60.814 63.158 0.00 0.00 40.09 3.16
7544 8597 1.813753 CTGTGGCGTCCGTAATGGG 60.814 63.158 0.00 0.00 38.76 4.00
7545 8598 3.199891 GTGGCGTCCGTAATGGGC 61.200 66.667 0.00 0.00 39.78 5.36
7546 8599 4.476752 TGGCGTCCGTAATGGGCC 62.477 66.667 0.00 0.00 43.40 5.80
7566 8619 2.035626 CCCATCTTGGCACGGGTT 59.964 61.111 0.00 0.00 35.79 4.11
7567 8620 2.342650 CCCATCTTGGCACGGGTTG 61.343 63.158 0.00 0.00 35.79 3.77
7568 8621 1.303236 CCATCTTGGCACGGGTTGA 60.303 57.895 0.00 0.00 0.00 3.18
7569 8622 1.586154 CCATCTTGGCACGGGTTGAC 61.586 60.000 0.00 0.00 0.00 3.18
7570 8623 1.303317 ATCTTGGCACGGGTTGACC 60.303 57.895 0.00 0.00 28.00 4.02
7571 8624 1.779061 ATCTTGGCACGGGTTGACCT 61.779 55.000 0.00 0.00 36.97 3.85
7572 8625 1.528309 CTTGGCACGGGTTGACCTT 60.528 57.895 0.00 0.00 36.97 3.50
7573 8626 1.076632 TTGGCACGGGTTGACCTTT 60.077 52.632 0.00 0.00 36.97 3.11
7574 8627 0.684805 TTGGCACGGGTTGACCTTTT 60.685 50.000 0.00 0.00 36.97 2.27
7575 8628 0.684805 TGGCACGGGTTGACCTTTTT 60.685 50.000 0.00 0.00 36.97 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.460987 GCAGCACTAATCGCACCTCT 60.461 55.000 0.00 0.00 0.00 3.69
1 2 0.460987 AGCAGCACTAATCGCACCTC 60.461 55.000 0.00 0.00 0.00 3.85
8 9 2.168521 TCCAGTACCAGCAGCACTAATC 59.831 50.000 0.00 0.00 0.00 1.75
78 79 9.713713 TTCTTAATAACAATTAACAAAAGGGGC 57.286 29.630 0.00 0.00 0.00 5.80
94 95 6.204882 ACAACTGCCTCACACTTCTTAATAAC 59.795 38.462 0.00 0.00 0.00 1.89
189 193 2.086054 ATGTCTCGTCAGAGTTTGGC 57.914 50.000 0.00 0.00 44.65 4.52
220 224 1.673168 CAGCTGGGCAGGTATTTCTC 58.327 55.000 5.57 0.00 37.39 2.87
263 273 2.681848 CACTGCTATTCCCTTGCAAGAG 59.318 50.000 28.05 15.54 35.17 2.85
264 274 2.715046 CACTGCTATTCCCTTGCAAGA 58.285 47.619 28.05 8.51 35.17 3.02
265 275 1.133790 GCACTGCTATTCCCTTGCAAG 59.866 52.381 19.93 19.93 35.17 4.01
266 276 1.176527 GCACTGCTATTCCCTTGCAA 58.823 50.000 0.00 0.00 35.17 4.08
312 322 0.163146 GACGCTAGTTTGACGTTGGC 59.837 55.000 0.00 0.00 40.69 4.52
513 535 2.989253 GGACCCAAAAGGCACGGG 60.989 66.667 0.00 0.00 46.22 5.28
646 669 5.012871 TCTGTCACTCCACAGTACTAGTACT 59.987 44.000 26.61 26.61 46.52 2.73
650 673 4.156922 CCTTCTGTCACTCCACAGTACTAG 59.843 50.000 0.00 0.00 43.80 2.57
651 674 4.079970 CCTTCTGTCACTCCACAGTACTA 58.920 47.826 0.00 0.00 43.80 1.82
652 675 2.894126 CCTTCTGTCACTCCACAGTACT 59.106 50.000 0.00 0.00 43.80 2.73
653 676 2.628657 ACCTTCTGTCACTCCACAGTAC 59.371 50.000 0.74 0.00 43.80 2.73
767 795 2.167398 GAGCACGGGGTGAGCTGTTA 62.167 60.000 0.00 0.00 45.06 2.41
768 796 3.537206 GAGCACGGGGTGAGCTGTT 62.537 63.158 0.00 0.00 45.06 3.16
770 798 2.351244 TAGAGCACGGGGTGAGCTG 61.351 63.158 0.00 0.00 45.06 4.24
772 800 2.184579 GTAGAGCACGGGGTGAGC 59.815 66.667 0.00 0.00 35.23 4.26
773 801 1.810532 GAGTAGAGCACGGGGTGAG 59.189 63.158 0.00 0.00 35.23 3.51
774 802 2.044555 CGAGTAGAGCACGGGGTGA 61.045 63.158 0.00 0.00 35.23 4.02
775 803 2.267681 GACGAGTAGAGCACGGGGTG 62.268 65.000 0.00 0.00 35.51 4.61
776 804 2.035312 ACGAGTAGAGCACGGGGT 59.965 61.111 0.00 0.00 35.51 4.95
784 814 3.305398 AAAAGCAGTGGACGAGTAGAG 57.695 47.619 0.00 0.00 0.00 2.43
785 815 3.746045 AAAAAGCAGTGGACGAGTAGA 57.254 42.857 0.00 0.00 0.00 2.59
809 839 0.038526 GGGCAGTTCGTTCGAGAAGA 60.039 55.000 0.00 0.00 0.00 2.87
926 959 4.664267 TGCCTGCCTGTCCCTCCT 62.664 66.667 0.00 0.00 0.00 3.69
1580 1631 2.222508 CCTAAACGCGTCATTCAACTCG 60.223 50.000 14.44 0.00 33.77 4.18
1586 1637 3.251571 AGAAGACCTAAACGCGTCATTC 58.748 45.455 14.44 9.29 0.00 2.67
1656 1708 9.901724 GAAACATAGTACTACATTCGTTCAATG 57.098 33.333 4.31 0.00 46.70 2.82
1711 1763 4.141233 AGCAAAAACTTCTGGCAAACAT 57.859 36.364 0.00 0.00 0.00 2.71
1989 2041 3.403038 TCTTTACTTGACAAGCTCAGGC 58.597 45.455 15.24 0.00 39.06 4.85
1990 2042 5.618640 GCATTCTTTACTTGACAAGCTCAGG 60.619 44.000 15.24 0.42 32.10 3.86
2008 2060 0.613260 TGAGGGTAAGTGCGCATTCT 59.387 50.000 15.91 3.36 0.00 2.40
2009 2061 1.009829 CTGAGGGTAAGTGCGCATTC 58.990 55.000 15.91 0.17 0.00 2.67
2014 2066 2.009774 CAAATCCTGAGGGTAAGTGCG 58.990 52.381 0.00 0.00 0.00 5.34
2017 2069 8.585018 CAAAAATTACAAATCCTGAGGGTAAGT 58.415 33.333 0.00 0.00 0.00 2.24
2026 2078 8.497554 CACACAATCCAAAAATTACAAATCCTG 58.502 33.333 0.00 0.00 0.00 3.86
2094 2146 4.385199 CCCCTAATAGGTTCATTGCTGTCA 60.385 45.833 5.49 0.00 31.93 3.58
2120 2172 9.727627 GATGTGTTACTTGGTACTACTATGTAC 57.272 37.037 0.00 0.00 41.31 2.90
2121 2173 9.465199 TGATGTGTTACTTGGTACTACTATGTA 57.535 33.333 0.00 0.00 0.00 2.29
2122 2174 8.357290 TGATGTGTTACTTGGTACTACTATGT 57.643 34.615 0.00 0.00 0.00 2.29
2138 2190 8.744568 TTATGCATAGGTTCATTGATGTGTTA 57.255 30.769 6.50 0.00 0.00 2.41
2237 2289 9.877178 AAATAAGTGGATAAAACACACACAAAA 57.123 25.926 0.00 0.00 41.21 2.44
2312 2364 9.573133 GGTCATGTTGTAAGGAAGAATAAAATG 57.427 33.333 0.00 0.00 0.00 2.32
2333 2385 6.842676 AGTTGGTTTTCTAAGAAGAGGTCAT 58.157 36.000 0.00 0.00 31.96 3.06
2914 2966 4.089361 AGGGGAACAAAGCAATTTCTAGG 58.911 43.478 0.00 0.00 0.00 3.02
2917 2969 6.493189 TTAAAGGGGAACAAAGCAATTTCT 57.507 33.333 0.00 0.00 0.00 2.52
2918 2970 6.765989 ACTTTAAAGGGGAACAAAGCAATTTC 59.234 34.615 19.14 0.00 32.44 2.17
3048 3100 5.106317 ACCAAATCACAAACATCGACCATAC 60.106 40.000 0.00 0.00 0.00 2.39
3367 3503 4.724074 ACCACAAAATGCATGTATCCAG 57.276 40.909 0.00 0.00 0.00 3.86
3368 3504 5.451659 GCATACCACAAAATGCATGTATCCA 60.452 40.000 0.00 0.00 46.19 3.41
3513 3809 8.383175 TCAACTTTCATCCTACTCCTGTAAAAT 58.617 33.333 0.00 0.00 0.00 1.82
3733 4147 9.436957 CAACTTGTAGTAAGGTCTGAACATATT 57.563 33.333 0.00 0.00 0.00 1.28
3839 4257 6.624352 ACAATGTGGATTGACACTATATGC 57.376 37.500 0.00 0.00 41.49 3.14
3841 4259 8.489489 AGAGAACAATGTGGATTGACACTATAT 58.511 33.333 0.00 0.00 41.49 0.86
4048 4466 9.110502 GATAATGTTCGAAGTTAGAAGGGAAAT 57.889 33.333 0.00 0.00 0.00 2.17
4141 4559 2.998670 CGATTGAGAAAGCAGAAGCAGA 59.001 45.455 0.00 0.00 45.49 4.26
4187 4605 5.280164 GGACCAAGCCATACATGATCATCTA 60.280 44.000 4.86 0.00 0.00 1.98
4566 4984 8.451748 GTCTGGTAGCTAAGAAACAATTAAAGG 58.548 37.037 0.00 0.00 0.00 3.11
4696 5442 7.016268 CCCACTGGACAATACTACCAACTATAT 59.984 40.741 0.00 0.00 33.14 0.86
4777 5524 8.264347 TGATGACTAATTAACAGGCTCATAACA 58.736 33.333 0.00 0.00 0.00 2.41
4930 5945 4.234574 GCATTGTACAAAGGCCTAACAAC 58.765 43.478 19.33 11.56 33.27 3.32
4954 5969 1.650528 AGCACCTCTCTTAAGCACCT 58.349 50.000 0.00 0.00 0.00 4.00
4955 5970 2.079925 CAAGCACCTCTCTTAAGCACC 58.920 52.381 0.00 0.00 0.00 5.01
4956 5971 2.079925 CCAAGCACCTCTCTTAAGCAC 58.920 52.381 0.00 0.00 0.00 4.40
4957 5972 1.977854 TCCAAGCACCTCTCTTAAGCA 59.022 47.619 0.00 0.00 0.00 3.91
4958 5973 2.234908 TCTCCAAGCACCTCTCTTAAGC 59.765 50.000 0.00 0.00 0.00 3.09
4959 5974 4.543590 TTCTCCAAGCACCTCTCTTAAG 57.456 45.455 0.00 0.00 0.00 1.85
4960 5975 4.974645 TTTCTCCAAGCACCTCTCTTAA 57.025 40.909 0.00 0.00 0.00 1.85
4961 5976 6.620877 TTATTTCTCCAAGCACCTCTCTTA 57.379 37.500 0.00 0.00 0.00 2.10
4962 5977 5.505181 TTATTTCTCCAAGCACCTCTCTT 57.495 39.130 0.00 0.00 0.00 2.85
4963 5978 5.249420 GTTTATTTCTCCAAGCACCTCTCT 58.751 41.667 0.00 0.00 0.00 3.10
4964 5979 4.396478 GGTTTATTTCTCCAAGCACCTCTC 59.604 45.833 0.00 0.00 0.00 3.20
4965 5980 4.202567 TGGTTTATTTCTCCAAGCACCTCT 60.203 41.667 0.00 0.00 0.00 3.69
4966 5981 4.079253 TGGTTTATTTCTCCAAGCACCTC 58.921 43.478 0.00 0.00 0.00 3.85
5005 6020 1.400494 GCCCTGTACAAATAAGCACCG 59.600 52.381 0.00 0.00 0.00 4.94
5028 6043 3.124560 GGAGAGACGCCTAATTAAGCAC 58.875 50.000 6.85 0.51 0.00 4.40
5029 6044 3.031736 AGGAGAGACGCCTAATTAAGCA 58.968 45.455 6.85 0.00 30.33 3.91
5042 6057 4.647399 AGTGCCTATTTCTACAGGAGAGAC 59.353 45.833 0.00 0.00 34.93 3.36
5082 6097 7.110155 AGGAGATGCTTAGAAAAATAAACCGA 58.890 34.615 0.00 0.00 0.00 4.69
5107 6122 4.941263 CCTTGTACAATGCTAGGTGCTTAA 59.059 41.667 9.13 0.00 43.37 1.85
5263 6279 7.200455 TCATACACTGTAATACGACTTCATGG 58.800 38.462 0.00 0.00 0.00 3.66
5616 6635 1.732259 CCCAAAGAAATCAGACCGTCG 59.268 52.381 0.00 0.00 0.00 5.12
5675 6694 6.716628 TCATACTGTTCCAAAGCAGAGAAAAT 59.283 34.615 0.00 0.00 36.62 1.82
5731 6750 6.435904 CAGGTAAAATTTGACCCCAGACAATA 59.564 38.462 19.68 0.00 36.27 1.90
5791 6810 4.054369 TCAGGGATGGAAGGTATGGATTT 58.946 43.478 0.00 0.00 0.00 2.17
6089 7111 0.383590 TGAGATGCGCAGAGAGTAGC 59.616 55.000 18.32 0.00 0.00 3.58
6132 7154 6.787458 TCCCTAGACTATCAGGATTGCATTTA 59.213 38.462 0.00 0.00 33.42 1.40
6140 7162 4.171044 AGGTGTTCCCTAGACTATCAGGAT 59.829 45.833 0.00 0.00 43.87 3.24
6445 7481 4.141620 TGCTCCTCAGGATGGAAATAGAAC 60.142 45.833 0.00 0.00 36.16 3.01
6486 7522 1.902508 CAGGAAGACTGGGTAAGCAGA 59.097 52.381 0.00 0.00 43.70 4.26
6616 7652 2.855180 CAGAAAGCCTGTGTTATTGCG 58.145 47.619 0.00 0.00 38.10 4.85
7078 8116 7.254852 CAGTAAAAAGACAACAGCCAAACTTA 58.745 34.615 0.00 0.00 0.00 2.24
7188 8235 3.819337 GAGATGTGGCACTTGATATGCAT 59.181 43.478 19.83 3.79 45.27 3.96
7195 8242 2.936919 ACAAGAGATGTGGCACTTGA 57.063 45.000 19.83 0.00 41.93 3.02
7247 8295 3.064545 GTGTCATAATCAGACAAGGCAGC 59.935 47.826 0.00 0.00 46.50 5.25
7319 8372 0.750850 TAAGCGGCACATAGGAGGTC 59.249 55.000 1.45 0.00 0.00 3.85
7320 8373 1.424638 ATAAGCGGCACATAGGAGGT 58.575 50.000 1.45 0.00 0.00 3.85
7321 8374 2.146342 CAATAAGCGGCACATAGGAGG 58.854 52.381 1.45 0.00 0.00 4.30
7322 8375 1.532868 GCAATAAGCGGCACATAGGAG 59.467 52.381 1.45 0.00 0.00 3.69
7323 8376 1.593196 GCAATAAGCGGCACATAGGA 58.407 50.000 1.45 0.00 0.00 2.94
7334 8387 0.811281 AACTCCTTGCCGCAATAAGC 59.189 50.000 6.19 0.00 40.87 3.09
7335 8388 1.468054 GCAACTCCTTGCCGCAATAAG 60.468 52.381 6.19 9.47 46.27 1.73
7336 8389 0.525761 GCAACTCCTTGCCGCAATAA 59.474 50.000 6.19 0.00 46.27 1.40
7337 8390 2.179764 GCAACTCCTTGCCGCAATA 58.820 52.632 6.19 0.00 46.27 1.90
7338 8391 2.964978 GCAACTCCTTGCCGCAAT 59.035 55.556 6.19 0.00 46.27 3.56
7345 8398 2.582728 TGCAAAACTGCAACTCCTTG 57.417 45.000 0.00 0.00 42.40 3.61
7354 8407 2.094417 GTCGTCTCCTATGCAAAACTGC 59.906 50.000 0.00 0.00 0.00 4.40
7355 8408 3.589988 AGTCGTCTCCTATGCAAAACTG 58.410 45.455 0.00 0.00 0.00 3.16
7356 8409 3.258372 TGAGTCGTCTCCTATGCAAAACT 59.742 43.478 7.21 0.00 39.75 2.66
7357 8410 3.368236 GTGAGTCGTCTCCTATGCAAAAC 59.632 47.826 7.21 0.00 39.75 2.43
7358 8411 3.585862 GTGAGTCGTCTCCTATGCAAAA 58.414 45.455 7.21 0.00 39.75 2.44
7359 8412 2.094182 GGTGAGTCGTCTCCTATGCAAA 60.094 50.000 7.21 0.00 39.75 3.68
7360 8413 1.476891 GGTGAGTCGTCTCCTATGCAA 59.523 52.381 7.21 0.00 39.75 4.08
7361 8414 1.103803 GGTGAGTCGTCTCCTATGCA 58.896 55.000 7.21 0.00 39.75 3.96
7362 8415 1.335496 GAGGTGAGTCGTCTCCTATGC 59.665 57.143 7.21 0.00 45.08 3.14
7363 8416 1.950909 GGAGGTGAGTCGTCTCCTATG 59.049 57.143 18.85 0.00 45.08 2.23
7364 8417 1.475392 CGGAGGTGAGTCGTCTCCTAT 60.475 57.143 21.72 0.00 45.08 2.57
7365 8418 0.107800 CGGAGGTGAGTCGTCTCCTA 60.108 60.000 21.72 0.00 45.08 2.94
7367 8420 3.053849 GCGGAGGTGAGTCGTCTCC 62.054 68.421 17.09 17.09 42.60 3.71
7368 8421 2.259875 CTGCGGAGGTGAGTCGTCTC 62.260 65.000 2.47 2.47 40.79 3.36
7369 8422 2.282251 TGCGGAGGTGAGTCGTCT 60.282 61.111 0.00 0.00 0.00 4.18
7370 8423 1.863662 TTCTGCGGAGGTGAGTCGTC 61.864 60.000 3.37 0.00 0.00 4.20
7371 8424 1.251527 ATTCTGCGGAGGTGAGTCGT 61.252 55.000 3.37 0.00 0.00 4.34
7372 8425 0.803768 CATTCTGCGGAGGTGAGTCG 60.804 60.000 3.37 0.00 0.00 4.18
7373 8426 0.532573 TCATTCTGCGGAGGTGAGTC 59.467 55.000 3.37 0.00 0.00 3.36
7374 8427 0.976641 TTCATTCTGCGGAGGTGAGT 59.023 50.000 3.37 0.00 0.00 3.41
7375 8428 2.099141 TTTCATTCTGCGGAGGTGAG 57.901 50.000 3.37 0.00 0.00 3.51
7376 8429 2.559698 TTTTCATTCTGCGGAGGTGA 57.440 45.000 3.37 6.47 0.00 4.02
7377 8430 3.728864 CGATTTTTCATTCTGCGGAGGTG 60.729 47.826 3.37 3.96 0.00 4.00
7378 8431 2.420022 CGATTTTTCATTCTGCGGAGGT 59.580 45.455 3.37 0.00 0.00 3.85
7379 8432 2.792542 GCGATTTTTCATTCTGCGGAGG 60.793 50.000 3.37 0.00 0.00 4.30
7380 8433 2.159531 TGCGATTTTTCATTCTGCGGAG 60.160 45.455 0.00 0.00 0.00 4.63
7381 8434 1.809547 TGCGATTTTTCATTCTGCGGA 59.190 42.857 0.00 0.00 0.00 5.54
7382 8435 2.261037 TGCGATTTTTCATTCTGCGG 57.739 45.000 0.00 0.00 0.00 5.69
7383 8436 4.627923 TTTTGCGATTTTTCATTCTGCG 57.372 36.364 0.00 0.00 0.00 5.18
7384 8437 8.931905 TTTATTTTTGCGATTTTTCATTCTGC 57.068 26.923 0.00 0.00 0.00 4.26
7392 8445 9.216087 CGTTTTCCTTTTATTTTTGCGATTTTT 57.784 25.926 0.00 0.00 0.00 1.94
7393 8446 8.391859 ACGTTTTCCTTTTATTTTTGCGATTTT 58.608 25.926 0.00 0.00 0.00 1.82
7394 8447 7.911343 ACGTTTTCCTTTTATTTTTGCGATTT 58.089 26.923 0.00 0.00 0.00 2.17
7395 8448 7.471657 ACGTTTTCCTTTTATTTTTGCGATT 57.528 28.000 0.00 0.00 0.00 3.34
7396 8449 7.341446 CAACGTTTTCCTTTTATTTTTGCGAT 58.659 30.769 0.00 0.00 0.00 4.58
7397 8450 6.237861 CCAACGTTTTCCTTTTATTTTTGCGA 60.238 34.615 0.00 0.00 0.00 5.10
7398 8451 5.899151 CCAACGTTTTCCTTTTATTTTTGCG 59.101 36.000 0.00 0.00 0.00 4.85
7399 8452 6.684979 CACCAACGTTTTCCTTTTATTTTTGC 59.315 34.615 0.00 0.00 0.00 3.68
7400 8453 7.183433 CCACCAACGTTTTCCTTTTATTTTTG 58.817 34.615 0.00 0.00 0.00 2.44
7401 8454 6.183360 GCCACCAACGTTTTCCTTTTATTTTT 60.183 34.615 0.00 0.00 0.00 1.94
7402 8455 5.294799 GCCACCAACGTTTTCCTTTTATTTT 59.705 36.000 0.00 0.00 0.00 1.82
7403 8456 4.812091 GCCACCAACGTTTTCCTTTTATTT 59.188 37.500 0.00 0.00 0.00 1.40
7404 8457 4.373527 GCCACCAACGTTTTCCTTTTATT 58.626 39.130 0.00 0.00 0.00 1.40
7405 8458 3.243941 GGCCACCAACGTTTTCCTTTTAT 60.244 43.478 0.00 0.00 0.00 1.40
7406 8459 2.101082 GGCCACCAACGTTTTCCTTTTA 59.899 45.455 0.00 0.00 0.00 1.52
7407 8460 1.134640 GGCCACCAACGTTTTCCTTTT 60.135 47.619 0.00 0.00 0.00 2.27
7408 8461 0.462375 GGCCACCAACGTTTTCCTTT 59.538 50.000 0.00 0.00 0.00 3.11
7409 8462 1.730451 CGGCCACCAACGTTTTCCTT 61.730 55.000 2.24 0.00 0.00 3.36
7410 8463 2.190841 CGGCCACCAACGTTTTCCT 61.191 57.895 2.24 0.00 0.00 3.36
7411 8464 2.333581 CGGCCACCAACGTTTTCC 59.666 61.111 2.24 0.00 0.00 3.13
7412 8465 2.333581 CCGGCCACCAACGTTTTC 59.666 61.111 2.24 0.00 0.00 2.29
7413 8466 2.440613 ACCGGCCACCAACGTTTT 60.441 55.556 0.00 0.00 0.00 2.43
7414 8467 3.213402 CACCGGCCACCAACGTTT 61.213 61.111 0.00 0.00 0.00 3.60
7445 8498 3.014085 TAGGAAGCAACCGGCCGAG 62.014 63.158 30.73 19.69 46.50 4.63
7446 8499 2.998480 TAGGAAGCAACCGGCCGA 60.998 61.111 30.73 0.00 46.50 5.54
7447 8500 2.818274 GTAGGAAGCAACCGGCCG 60.818 66.667 21.04 21.04 46.50 6.13
7448 8501 2.818274 CGTAGGAAGCAACCGGCC 60.818 66.667 0.00 0.00 46.50 6.13
7449 8502 2.047560 ACGTAGGAAGCAACCGGC 60.048 61.111 0.00 0.00 45.30 6.13
7450 8503 1.447314 GGACGTAGGAAGCAACCGG 60.447 63.158 0.00 0.00 34.73 5.28
7451 8504 1.804326 CGGACGTAGGAAGCAACCG 60.804 63.158 0.00 0.00 34.73 4.44
7452 8505 2.098831 GCGGACGTAGGAAGCAACC 61.099 63.158 0.00 0.00 0.00 3.77
7453 8506 0.739813 ATGCGGACGTAGGAAGCAAC 60.740 55.000 6.90 0.00 41.37 4.17
7454 8507 0.036765 AATGCGGACGTAGGAAGCAA 60.037 50.000 6.90 0.00 41.37 3.91
7455 8508 0.036765 AAATGCGGACGTAGGAAGCA 60.037 50.000 0.00 0.00 42.28 3.91
7456 8509 0.651031 GAAATGCGGACGTAGGAAGC 59.349 55.000 0.00 0.00 0.00 3.86
7457 8510 1.134788 AGGAAATGCGGACGTAGGAAG 60.135 52.381 0.00 0.00 0.00 3.46
7458 8511 0.899720 AGGAAATGCGGACGTAGGAA 59.100 50.000 0.00 0.00 0.00 3.36
7459 8512 1.766494 TAGGAAATGCGGACGTAGGA 58.234 50.000 0.00 0.00 0.00 2.94
7460 8513 2.814280 ATAGGAAATGCGGACGTAGG 57.186 50.000 0.00 0.00 0.00 3.18
7461 8514 4.025979 GTCAAATAGGAAATGCGGACGTAG 60.026 45.833 0.00 0.00 0.00 3.51
7462 8515 3.866910 GTCAAATAGGAAATGCGGACGTA 59.133 43.478 0.00 0.00 0.00 3.57
7463 8516 2.676342 GTCAAATAGGAAATGCGGACGT 59.324 45.455 0.00 0.00 0.00 4.34
7464 8517 2.285602 CGTCAAATAGGAAATGCGGACG 60.286 50.000 0.00 0.00 40.45 4.79
7465 8518 2.538939 GCGTCAAATAGGAAATGCGGAC 60.539 50.000 0.00 0.00 0.00 4.79
7466 8519 1.668751 GCGTCAAATAGGAAATGCGGA 59.331 47.619 0.00 0.00 0.00 5.54
7467 8520 1.268539 GGCGTCAAATAGGAAATGCGG 60.269 52.381 0.00 0.00 0.00 5.69
7468 8521 1.400142 TGGCGTCAAATAGGAAATGCG 59.600 47.619 0.00 0.00 0.00 4.73
7469 8522 2.163412 TGTGGCGTCAAATAGGAAATGC 59.837 45.455 0.00 0.00 0.00 3.56
7470 8523 3.181497 CCTGTGGCGTCAAATAGGAAATG 60.181 47.826 9.88 0.00 0.00 2.32
7471 8524 3.016736 CCTGTGGCGTCAAATAGGAAAT 58.983 45.455 9.88 0.00 0.00 2.17
7472 8525 2.432444 CCTGTGGCGTCAAATAGGAAA 58.568 47.619 9.88 0.00 0.00 3.13
7473 8526 1.948611 GCCTGTGGCGTCAAATAGGAA 60.949 52.381 17.46 0.00 39.62 3.36
7474 8527 0.392461 GCCTGTGGCGTCAAATAGGA 60.392 55.000 17.46 0.00 39.62 2.94
7475 8528 2.098293 GCCTGTGGCGTCAAATAGG 58.902 57.895 10.85 10.85 39.62 2.57
7485 8538 2.671619 TTAACTGGCGCCTGTGGC 60.672 61.111 35.62 5.89 46.75 5.01
7486 8539 2.677003 CGTTAACTGGCGCCTGTGG 61.677 63.158 35.62 21.91 0.00 4.17
7487 8540 1.959226 ACGTTAACTGGCGCCTGTG 60.959 57.895 35.62 25.42 0.00 3.66
7488 8541 1.959226 CACGTTAACTGGCGCCTGT 60.959 57.895 30.90 30.90 0.00 4.00
7489 8542 2.860293 CACGTTAACTGGCGCCTG 59.140 61.111 29.48 29.48 0.00 4.85
7490 8543 3.047877 GCACGTTAACTGGCGCCT 61.048 61.111 29.70 10.43 0.00 5.52
7491 8544 2.195123 AATGCACGTTAACTGGCGCC 62.195 55.000 22.73 22.73 0.00 6.53
7492 8545 0.386731 AAATGCACGTTAACTGGCGC 60.387 50.000 0.00 0.00 0.00 6.53
7493 8546 1.976045 GAAAATGCACGTTAACTGGCG 59.024 47.619 3.71 0.00 0.00 5.69
7494 8547 3.006659 TGAAAATGCACGTTAACTGGC 57.993 42.857 3.71 7.65 0.00 4.85
7495 8548 7.033292 GTTAATGAAAATGCACGTTAACTGG 57.967 36.000 16.71 0.00 41.37 4.00
7498 8551 6.639279 ACCAGTTAATGAAAATGCACGTTAAC 59.361 34.615 16.43 16.43 43.16 2.01
7499 8552 6.638873 CACCAGTTAATGAAAATGCACGTTAA 59.361 34.615 0.00 0.00 31.77 2.01
7500 8553 6.146216 CACCAGTTAATGAAAATGCACGTTA 58.854 36.000 0.00 0.00 31.77 3.18
7501 8554 4.981674 CACCAGTTAATGAAAATGCACGTT 59.018 37.500 0.00 0.00 31.77 3.99
7502 8555 4.545610 CACCAGTTAATGAAAATGCACGT 58.454 39.130 0.00 0.00 31.77 4.49
7503 8556 3.364621 GCACCAGTTAATGAAAATGCACG 59.635 43.478 0.00 0.00 31.77 5.34
7504 8557 3.679502 GGCACCAGTTAATGAAAATGCAC 59.320 43.478 0.00 0.00 31.77 4.57
7505 8558 3.577848 AGGCACCAGTTAATGAAAATGCA 59.422 39.130 0.00 0.00 31.77 3.96
7506 8559 3.928375 CAGGCACCAGTTAATGAAAATGC 59.072 43.478 0.00 0.00 31.77 3.56
7507 8560 4.925054 CACAGGCACCAGTTAATGAAAATG 59.075 41.667 0.00 0.00 32.93 2.32
7508 8561 4.021192 CCACAGGCACCAGTTAATGAAAAT 60.021 41.667 0.00 0.00 0.00 1.82
7509 8562 3.320541 CCACAGGCACCAGTTAATGAAAA 59.679 43.478 0.00 0.00 0.00 2.29
7510 8563 2.890311 CCACAGGCACCAGTTAATGAAA 59.110 45.455 0.00 0.00 0.00 2.69
7511 8564 2.513753 CCACAGGCACCAGTTAATGAA 58.486 47.619 0.00 0.00 0.00 2.57
7512 8565 2.198827 CCACAGGCACCAGTTAATGA 57.801 50.000 0.00 0.00 0.00 2.57
7524 8577 2.125269 ATTACGGACGCCACAGGC 60.125 61.111 0.00 0.00 46.75 4.85
7525 8578 1.813753 CCATTACGGACGCCACAGG 60.814 63.158 0.00 0.00 36.56 4.00
7526 8579 1.813753 CCCATTACGGACGCCACAG 60.814 63.158 0.00 0.00 36.56 3.66
7527 8580 2.266372 CCCATTACGGACGCCACA 59.734 61.111 0.00 0.00 36.56 4.17
7528 8581 3.199891 GCCCATTACGGACGCCAC 61.200 66.667 0.00 0.00 36.56 5.01
7529 8582 4.476752 GGCCCATTACGGACGCCA 62.477 66.667 0.00 0.00 40.80 5.69
7549 8602 2.035626 AACCCGTGCCAAGATGGG 59.964 61.111 0.00 0.00 46.61 4.00
7550 8603 1.303236 TCAACCCGTGCCAAGATGG 60.303 57.895 0.00 0.00 41.55 3.51
7551 8604 1.586154 GGTCAACCCGTGCCAAGATG 61.586 60.000 0.00 0.00 0.00 2.90
7552 8605 1.303317 GGTCAACCCGTGCCAAGAT 60.303 57.895 0.00 0.00 0.00 2.40
7553 8606 1.990160 AAGGTCAACCCGTGCCAAGA 61.990 55.000 0.00 0.00 38.74 3.02
7554 8607 1.106944 AAAGGTCAACCCGTGCCAAG 61.107 55.000 0.00 0.00 38.74 3.61
7555 8608 0.684805 AAAAGGTCAACCCGTGCCAA 60.685 50.000 0.00 0.00 38.74 4.52
7556 8609 0.684805 AAAAAGGTCAACCCGTGCCA 60.685 50.000 0.00 0.00 38.74 4.92
7557 8610 2.120765 AAAAAGGTCAACCCGTGCC 58.879 52.632 0.00 0.00 38.74 5.01


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.